some update (f4f7dff5) · Commits · Zhang Xin / star_SED

mergeFiles.py

0 → 100644

+57 −0

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		import numpy as np
		import os
		from astropy.table import Table

		multiFileDir = '/nfsdata/share/CSSOSDataProductsSims/C10_refCat/1/'


		mergeKeys = ['parallax1',
		'interSpec_nuv',
		'interSpec_u',
		'interSpec_g',
		'interSpec_r',
		'interSpec_i',
		'interSpec_z',
		'interSpec_y',
		'interSpec_2MASS_H',
		'interSpec_2MASS_J',
		'interSpec_2MASS_Ks',
		'interSpec_GAIA_GAIA3.G',
		'interSpec_GAIA_GAIA3.Gbp',
		'interSpec_GAIA_GAIA3.Grp',
		'interSpec_GALEX_GALEX.FUV',
		'interSpec_GALEX_GALEX.NUV',
		'interSpec_LSST_u',
		'interSpec_LSST_g',
		'interSpec_LSST_r',
		'interSpec_LSST_i',
		'interSpec_LSST_z',
		'interSpec_LSST_y',
		'interSpec_PAN-STARRS_PS1.g',
		'interSpec_PAN-STARRS_PS1.r',
		'interSpec_PAN-STARRS_PS1.i',
		'interSpec_PAN-STARRS_PS1.z',
		'interSpec_PAN-STARRS_PS1.y',
		'interSpec_SLOAN_SDSS.u',
		'interSpec_SLOAN_SDSS.g',
		'interSpec_SLOAN_SDSS.r',
		'interSpec_SLOAN_SDSS.i',
		'interSpec_SLOAN_SDSS.z']
		allFiles = os.listdir(multiFileDir)
		mergeTable = None
		outFn = ''
		for fn in allFiles:
		if 'fits' not in fn:
		continue
		if mergeTable is None:
		mergeTable = Table.read(os.path.join(multiFileDir,fn))
		outFn = os.path.join(multiFileDir,fn[0:25]+'.fits')
		else:
		tTab = Table.read(os.path.join(multiFileDir,fn))
		for key in mergeKeys:
		mergeTable[key] = mergeTable[key] + tTab[key]

		mergeTable.write(outFn,overwrite = True)

produceSED.py

+1 −1

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		@@ -339,7 +339,7 @@ def getABMAG(spec, bandpass_fn, sw=None, ew = None, bpass_type = 'fits'):
		throughtput = Table(th_dat, names=['WAVELENGTH','SENSITIVITY'])

		if sw is None or ew is None:
		thr_ids = throughtput['SENSITIVITY'] > 0.01
		thr_ids = throughtput['SENSITIVITY'] > 0.001
		sWave = np.floor(throughtput[thr_ids][0][0])
		eWave = np.ceil(throughtput[thr_ids][-1][0])
		else:

pycode.py

+13 −6

Original line number	Diff line number	Diff line
		@@ -119,32 +119,39 @@ for star in cat:
		iterNum = iterNum + 1
		continue
		# specTable = np.zeros([nwv,2])
		s=Star(star['mwmsc_logte'], star['mwmsc_logg'], star['mwmsc_mass'], star['mwmsc_av'], star['mwmsc_mu0'], star['mwmsc_z'])
		# s=Star(star['mwmsc_logte'], star['mwmsc_logg'], star['mwmsc_mass'], star['mwmsc_av'], star['mwmsc_mu0'], star['mwmsc_z'])
		try:
		s=Star(star['teff'], star['grav'], star['mass'], star['AV'], star['DM'], star['z_met'])
		except:
		iterNum = iterNum + 1
		continue
		# av stellarmass dm teff logg feh
		# 0.0464 0.7512 10.8000 3.6914 4.5952 0.0122
		# s=StarParm(obj.param['teff'], obj.param['logg'], obj.param['stellarMass'], obj.param['av'], obj.param['DM'], obj.param['feh'])
		# s=Star(3.6914, 4.5952, 0.7512, 0.0464, 10.8000, 0.0122)
		#print("star[logTe], star[logg], star[Mass], star[Av], star[mu0], star[Z]: ", star['logTe'], star['logg'], star['Mass'], star['Av'], star['mu0'], star['Z'])
		d.interpSingleStar(s, spec, wave)

		rv_c = star['mwmsc_vrad']/(atcons.c.value/1000.)
		rv_c = star['RV']/(atcons.c.value/1000.)
		# rv_c = star['mwmsc_vrad']/(atcons.c.value/1000.)
		Doppler_factor = np.sqrt((1+rv_c)/(1-rv_c))
		wave_RV = wave*Doppler_factor
		# specTable[:,0] = wave[:]
		# specTable[:,1] = spec[:]
		# print(spec[500:509])
		spec_out = Table(np.array([wave_RV, np.power(10,spec[:])]).T, names=('WAVELENGTH', 'FLUX'))
		spec_norm_phot = produceSED.produceNormSED_photon(inputSED = spec_out,mag_norm = star['mwmsc_gsmag'], norm_filter_thr_fn= 'data/throughputs/SDSS/SLOAN_SDSS.g.fits',ws = 1050, we = 23950)
		# spec_norm_phot = produceSED.produceNormSED_photon(inputSED = spec_out,mag_norm = star['mwmsc_gsmag'], norm_filter_thr_fn= 'data/throughputs/SDSS/SLOAN_SDSS.g.fits',ws = 1050, we = 23950)
		spec_norm_phot = produceSED.produceNormSED_photon(inputSED = spec_out,mag_norm = star['app_csst_g'], norm_filter_thr_fn= 'data/throughputs/CSST_n/g.Throughput.fits',ws = 1050, we = 23950)
		# spec_norm_phot = produceSED.produceNormSED_photon(inputSED = spec_out,mag_norm = 17.8360, norm_filter_thr_fn= 'data/throughputs/SDSS/SLOAN_SDSS.g.fits',ws = 1000, we = 24000)
		mags = produceSED.calculatCSSTMAG(spec = spec_norm_phot, throughput_dir = 'data/throughputs/CSST_n/',ws= 2000, we = 11000)

		# mags_others = produceSED.calculatCSSTMAG(spec = spec_norm_phot, throughput_dir = 'data/throughputs/filter_transp/',ws= 1050, we = 23950, filelist=filters_other, band_instr='other')
		mags_others = produceSED.calculatCSSTMAG(spec = spec_norm_phot, throughput_dir = 'data/throughputs/filter_transp/',ws= 1050, we = 23950, filelist=filters_other, band_instr='other')

		for fi in filters:
		res[fi][iterNum] = mags[fi]
		for fi in filters_other:
		res[fi][iterNum] = mags_others[fi]
		parallaxs[iterNum] = 1/(10*(star['mwmsc_mu0']0.2)/100)
		parallaxs[iterNum] = 1/(10*(star['DM']0.2)/100)
		iterNum = iterNum + 1
		# print(mags, mags_others)

		@@ -187,7 +194,7 @@ if rank == 0:
		for fi in filters_other:
		res[fi] = res[fi] + total_res[i][fi]
		parallaxs = parallaxs + total_parall[i]
		cat.add_column(np.round(parallaxs,5),name='parallax')
		cat.add_column(np.round(parallaxs,5),name='parallax1')
		for fi in filters:
		cat.add_column(np.round(res[fi],5),name='interSpec_'+fi)
		for fi in filters_other:

pycode_multi_file.py

0 → 100644

+244 −0

Original line number	Diff line number	Diff line
		'''
		Author: Zhang Xin zhangx@bao.ac.cn
		Date: 2024-01-02 13:34:39
		LastEditors: Zhang Xin zhangx@bao.ac.cn
		LastEditTime: 2024-03-25 13:51:33
		FilePath: /csst-simulation/Users/zhangxin/Work/SlitlessSim/CSST_SIM/Star_spec/csst_spec_interp_clean/code/pycode.py
		Description: 这是默认设置,请设置`customMade`, 打开koroFileHeader查看配置进行设置: https://github.com/OBKoro1/koro1FileHeader/wiki/%E9%85%8D%E7%BD%AE
		'''
		##运行下面在mac/linux下执行
		# cc -fPIC -shared main_singlestar.c -I/usr/include -I/usr/include/cfitsio -lcfitsio -lm -o test.dylib

		import os
		import numpy as np
		from astropy.io import fits
		import ctypes
		from astropy.table import Table
		import produceSED
		import astropy.constants as atcons
		import sys
		# from ctypes import *

		# struct STAR
		# {
		# float logte;
		# float logg;
		# //float logL;
		# float Mass;
		# float Av;
		# float mu0;
		# float Z;
		# //float mbolmag;
		# };

		class Star(ctypes.Structure):
		_fields_ = [
		('logte',ctypes.c_float),
		('logg',ctypes.c_float),
		('Mass',ctypes.c_float),
		('Av', ctypes.c_float),
		('mu0', ctypes.c_float),
		('Z', ctypes.c_float)]

		#CHANGE
		#topdir='/run/media/chen/1TS/dupe/gitlab/csst_spec_interp/'
		topdir='/home/zhangxin/CSST_SIM/star_spec/csst_spec_interp_clean/code/'
		code_name='test.so'

		d = ctypes.CDLL(os.path.join(topdir,code_name))
		d.loadSpecLibs.argtypes=[ctypes.c_char_p, ctypes.c_char_p]
		d.loadExts.argtypes=[ctypes.c_char_p]


		#######################################################################################
		#CHANGE
		#nwv = d.loadSpecLibs(str.encode(os.path.join(topdir,'file_CK04.par')),str.encode(topdir))
		#d.loadExts(str.encode(os.path.join(topdir,"spec/Ext_odonnell94_R3.1_CK04W.fits")))
		#TO
		nwv = d.loadSpecLibs(str.encode(os.path.join(topdir,'file_BT-Settl_CSST_wl1000-24000_R1000.par')),str.encode(topdir))
		d.loadExts(str.encode(os.path.join(topdir,"spec/Ext_odonnell94_R3.1_CSST_wl1000-24000_R1000.fits")))
		########################################################################################

		print("Done loading Exts")
		spec = (ctypes.c_float*nwv)()
		wave = (ctypes.c_float*nwv)()
		d.interpSingleStar.argtypes=[ctypes.Structure, ctypes.POINTER(ctypes.c_float)]


		'''
		#example for a single star
		#s=Star(3.620752, 4.701155, 0.599979, 0.067540, 11.200001, 0.008501)
		s=Star(3.9739766, 8.108173, 0.6525841, 0.077022046, 9.05, 0.024376422)
		#s=Star(3.9739766, 4.99, 0.6525841, 0.077022046, 9.05, 0.024376422)
		d.interpSingleStar(s, spec)
		spec_ = spec[:]
		print(spec[500:509])
		'''

		from astropy.table import Table

		if len(sys.argv) < 3:
		# print('usage:\n'+sys.argv[0]+' survey_result.txt')
		sys.exit(0)

		catalogFn = str(sys.argv[1])

		# catalogFn = "/nfsdata/share/CSSTsimInputCat_TH/C9_RA240_DECp30.fits"
		# catalogFn = "/home/zhangxin/CSST_SIM/star_spec/csst_spec_interp_clean/code/data/catalog/trilegal.fits"
		outdir = str(sys.argv[2])
		# outFn = "C9_RA240_DECp30_refCat_1.fits"

		# outFn = catalogFn.strip().split('/')[-1][0:-5] + "_refCat_1.fits"
		cat = Table.read(catalogFn)
		# ids1 = cat['app_SDSS_g'] <= 22
		# ids2 = cat[ids1]['components'] == -1
		# cat = cat[ids1][ids2]

		filters = ['nuv','u','g','r','i','z','y']
		filters_other = ['2MASS_H','2MASS_J','2MASS_Ks','GAIA_GAIA3.G','GAIA_GAIA3.Gbp','GAIA_GAIA3.Grp','GALEX_GALEX.FUV','GALEX_GALEX.NUV','LSST_u','LSST_g','LSST_r','LSST_i','LSST_z','LSST_y','PAN-STARRS_PS1.g','PAN-STARRS_PS1.r','PAN-STARRS_PS1.i','PAN-STARRS_PS1.z','PAN-STARRS_PS1.y','SLOAN_SDSS.u','SLOAN_SDSS.g','SLOAN_SDSS.r','SLOAN_SDSS.i','SLOAN_SDSS.z']
		res = {}

		nrows = len(cat)
		for fi in filters:
		res[fi] = np.zeros(nrows)
		for fi in filters_other:
		res[fi] = np.zeros(nrows)

		parallaxs = np.zeros(nrows)

		from mpi4py import MPI
		comm = MPI.COMM_WORLD
		rank = comm.Get_rank()
		rank_size = comm.Get_size()
		print("------------------",rank_size, rank, nrows)
		outFn = catalogFn.strip().split('/')[-1][0:-5] + "_refCat_rank" + str(rank).rjust(2,'0') + ".fits"
		outFn1 = catalogFn.strip().split('/')[-1][0:-5] + "_refCat_rank" + str(rank).rjust(2,'0') + ".log"
		logf = open(os.path.join(outdir,outFn1), 'w')
		logf.write('This file exist!\n')
		logf.flush()
		logf.close()
		iterNum = 0
		max_wave = 23950
		for star in cat:
		if iterNum%10000==0:
		print(iterNum)
		# if iterNum > 100:
		# iterNum = iterNum + 1
		# continue
		if iterNum % rank_size != rank:
		iterNum = iterNum + 1
		continue
		# specTable = np.zeros([nwv,2])
		# s=Star(star['mwmsc_logte'], star['mwmsc_logg'], star['mwmsc_mass'], star['mwmsc_av'], star['mwmsc_mu0'], star['mwmsc_z'])
		try:
		s=Star(star['teff'], star['grav'], star['mass'], star['AV'], star['DM'], star['z_met'])
		except:
		iterNum = iterNum + 1
		continue
		# av stellarmass dm teff logg feh
		# 0.0464 0.7512 10.8000 3.6914 4.5952 0.0122
		# s=StarParm(obj.param['teff'], obj.param['logg'], obj.param['stellarMass'], obj.param['av'], obj.param['DM'], obj.param['feh'])
		# s=Star(3.6914, 4.5952, 0.7512, 0.0464, 10.8000, 0.0122)
		#print("star[logTe], star[logg], star[Mass], star[Av], star[mu0], star[Z]: ", star['logTe'], star['logg'], star['Mass'], star['Av'], star['mu0'], star['Z'])
		d.interpSingleStar(s, spec, wave)
		rv_c = star['RV']/(atcons.c.value/1000.)
		# rv_c = star['mwmsc_vrad']/(atcons.c.value/1000.)
		Doppler_factor = np.sqrt((1+rv_c)/(1-rv_c))
		wave_RV = wave*Doppler_factor
		if wave_RV[-1] < max_wave:
		continue
		# specTable[:,0] = wave[:]
		# specTable[:,1] = spec[:]
		# print(spec[500:509])
		spec_out = Table(np.array([wave_RV, np.power(10,spec[:])]).T, names=('WAVELENGTH', 'FLUX'))
		# spec_norm_phot = produceSED.produceNormSED_photon(inputSED = spec_out,mag_norm = star['mwmsc_gsmag'], norm_filter_thr_fn= 'data/throughputs/SDSS/SLOAN_SDSS.g.fits',ws = 1050, we = 23950)
		spec_norm_phot = produceSED.produceNormSED_photon(inputSED = spec_out,mag_norm = star['app_SDSS_g'], norm_filter_thr_fn= 'data/throughputs/SDSS/SLOAN_SDSS.g.fits',ws = 1050, we = 23950)
		# spec_norm_phot = produceSED.produceNormSED_photon(inputSED = spec_out,mag_norm = 17.8360, norm_filter_thr_fn= 'data/throughputs/SDSS/SLOAN_SDSS.g.fits',ws = 1000, we = 24000)
		mags = produceSED.calculatCSSTMAG(spec = spec_norm_phot, throughput_dir = 'data/throughputs/CSST_n/',ws= 2000, we = 11000)

		# mags_others = produceSED.calculatCSSTMAG(spec = spec_norm_phot, throughput_dir = 'data/throughputs/filter_transp/',ws= 1050, we = 23950, filelist=filters_other, band_instr='other')
		mags_others = produceSED.calculatCSSTMAG(spec = spec_norm_phot, throughput_dir = 'data/throughputs/filter_transp/',ws= 1050, we = max_wave, filelist=filters_other, band_instr='other')

		for fi in filters:
		res[fi][iterNum] = mags[fi]
		for fi in filters_other:
		res[fi][iterNum] = mags_others[fi]
		parallaxs[iterNum] = 1/(10*(star['DM']0.2)/100)
		iterNum = iterNum + 1
		# print(mags, mags_others)

		# send_data1 = res
		# send_data2 = parallaxs
		# if rank == 0:
		# total_res = comm.gather(send_data1, root=0)
		# total_parall = comm.gather(send_data2, root=0)

		# for i in np.arange(1, rank_size, 1):
		# for fi in filters:
		# res[fi] = res[fi] + total_res[i][fi]
		# for fi in filters_other:
		# res[fi] = res[fi] + total_res[i][fi]
		# parallaxs = parallaxs + total_parall[i]
		# cat.add_column(np.round(parallaxs,5),name='parallax')
		# for fi in filters:
		# cat.add_column(np.round(res[fi],5),name='interSpec_'+fi)
		# for fi in filters_other:
		# cat.add_column(np.round(res[fi],5),name='interSpec_'+fi)
		# outdir = '/nfsdata/share/CSSOSDataProductsSims/trilegalCat/'
		# outFn = "C9_RA300_DECm60_refCat.fits"
		# cat.write(os.path.join(outdir,outFn),overwrite=True)

		# else:
		# comm.gather(send_data1, root=0)
		# comm.gather(send_data2, root=0)
		cat.add_column(np.round(parallaxs,5),name='parallax1')
		for fi in filters:
		cat.add_column(np.round(res[fi],5),name='interSpec_'+fi)
		for fi in filters_other:
		cat.add_column(np.round(res[fi],5),name='interSpec_'+fi)
		cat.write(os.path.join(outdir,outFn),overwrite=True)
		# total_res=comm.gather(res, root=0)
		# total_parall = comm.gather(parallaxs, root=0)

		# if rank == 0:
		# # new_res = res
		# # total_res=comm.gather(res, root=0)
		# # print("gather data size is ", size(total_res))
		# for i in np.arange(1, rank_size, 1):
		# for fi in filters:
		# res[fi] = res[fi] + total_res[i][fi]
		# for fi in filters_other:
		# res[fi] = res[fi] + total_res[i][fi]
		# parallaxs = parallaxs + total_parall[i]
		# cat.add_column(np.round(parallaxs,5),name='parallax1')
		# for fi in filters:
		# cat.add_column(np.round(res[fi],5),name='interSpec_'+fi)
		# for fi in filters_other:
		# cat.add_column(np.round(res[fi],5),name='interSpec_'+fi)
		# # outdir = '/nfsdata/share/CSSOSDataProductsSims/trilegalCat/'
		# # outFn = "C9_RA240_DECp30_refCat_1.fits"
		# cat.write(os.path.join(outdir,outFn),overwrite=True)
		# print('--------------------------')
		# print(mags['nuv']-star['mwmsc_nuvmag'], mags['u']-star['mwmsc_umag'], mags['g']-star['mwmsc_gmag'], mags['r']-star['mwmsc_rmag'], mags['i']-star['mwmsc_imag'],mags['z']-star['mwmsc_zmag'],mags['y']-star['mwmsc_ymag'])
		#exmple of handling a fits catalouge with many stars
		#wvs=fits.open('spec/fp00k2odfnew.fits')[2].data['wave'] #in Angstrom
		# cat_list=np.loadtxt(topdir+'cat.list', dtype='U')
		# for listfile in cat_list:
		# hdu = fits.open(topdir+listfile)
		# cat=hdu[1].data
		# for star in cat:
		# specTable = np.zeros([nwv,2])
		# s=Star(star['logTe'], star['logg'], star['Mass'], star['Av'], star['mu0'], star['Z'])
		# #print("star[logTe], star[logg], star[Mass], star[Av], star[mu0], star[Z]: ", star['logTe'], star['logg'], star['Mass'], star['Av'], star['mu0'], star['Z'])
		# d.interpSingleStar(s, spec, wave)
		# specTable[:,0] = wave[:]
		# specTable[:,1] = spec[:]
		# # print(spec[500:509])
		# spec_out = Table(np.array([wave[:], np.power(10,spec[:])]).T, names=('WAVELENGTH', 'FLUX'))
		# spec_norm_phot = produceSED.produceNormSED_photon(inputSED = spec_out,mag_norm = 24.0, norm_filter_thr_fn= 'data/throughputs/SDSS/SLOAN_SDSS.g.fits',ws = 2500, we = 10000)
		# mags = produceSED.calculatCSSTMAG(spec = spec_norm_phot, throughput_dir = 'data/throughputs/CSST/',ws= 2500, we = 10000)

		# # print("MAG is ",mags)
		# print('--------------------------')
		# print(mags['nuv']-star['mwmsc_nuvmag'], mag['u']-star['mwmsc_umag'], mag['g']-star['mwmsc_gmag'], mag['r']-star['mwmsc_rmag'], mag['i']-star['mwmsc_imag'],mag['z']-star['mwmsc_zmag'],mag['y']-star['mwmsc_ymag'])

test.so

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